BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013230.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,881,403 number of mapped reads = 2,565,360 (89.03%) number of supplementary alignments = 11,828 (0.41%) number of secondary alignments = 0 number of mapped bases = 172,628,568 bp number of sequenced bases = 172,554,714 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,434 duplication rate = 3.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5829 >>>>>>> ACTG content number of A's = 48,283,620 bp (27.98%) number of C's = 31,416,237 bp (18.21%) number of T's = 55,210,462 bp (32%) number of G's = 37,606,486 bp (21.79%) number of N's = 37,909 bp (0.02%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,411,862 number of insertions = 13,020 mapped reads with insertion percentage = 0.5% number of deletions = 43,170 mapped reads with deletion percentage = 1.66% homopolymer indels = 46.16% >>>>>>> Coverage mean coverageData = 0.0558X std coverageData = 0.5846X There is a 4.65% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 14069715 0.05644806397493389 0.9574582016199656 chr2 243199373 17253965 0.07094576267678124 0.682789365338685 chr3 198022430 11688931 0.059028318155675594 0.2785109225338915 chr4 191154276 14718377 0.07699737253065686 0.34376839374360824 chr5 180915260 9037046 0.04995181722094642 0.261683935497811 chr6 171115067 13752435 0.0803695153273674 0.46133736524012675 chr7 159138663 10003392 0.06285959559682866 1.043853468343092 chr8 146364022 7533346 0.05146993022643229 0.6692520531261978 chr9 141213431 8636314 0.0611578795220973 0.504840563323672 chr10 135534747 5900403 0.043534245871282 0.654656473025782 chr11 135006516 5218425 0.03865313434204909 0.3396828717101455 chr12 133851895 8001219 0.05977665837304731 0.29628563275890407 chr13 115169878 3441573 0.029882579193146318 0.2043665216279499 chr14 107349540 8136465 0.0757941300912887 0.3564069921033105 chr15 102531392 3045101 0.02969920665858121 0.19599053366505936 chr16 90354753 4748245 0.05255113696121774 0.31733363011454646 chr17 81195210 5822849 0.07171419348505903 0.33226695267022827 chr18 78077248 4883523 0.06254732492620642 1.0129782846611 chr19 59128983 2729186 0.04615648471410374 0.6873208555857002 chr20 63025520 2742678 0.04351694361268261 0.2550525283895098 chr21 48129895 2985390 0.06202776881187877 0.3148965740223445 chr22 51304566 2234127 0.043546358037606245 0.23785467903141733 chrMT 16571 1080259 65.18972904471667 40.09578802285361 chrX 155270560 4684908 0.030172545265503004 0.24967913364075092 chrY 59373566 280696 0.00472762575857411 0.15676717811537919